/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/

//  Software Guide : BeginLatex
//
//  In order to initialize deformable registration algorithm it is often
//  convenient to generate a displacemnt field from a set of feature
//  correspondances provided by the user. The following example illustrates how
//  to use the \doxygen{itkLandmarkDisplacementFieldSource} class in order to generate a
//  displacement field from the specification of two sets of landmarks.
//  Landmarks from one set are associated one-to-one to the landmarks in the
//  other set. Each landmark pair defines one displacement vector. This class
//  interpolates the values of all other displacement vectors using
//  \doxygen{KernelBasedTransform}
//
//
//  \index{Registration!Finite Element-Based}
//
//  Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"

#include "itkImage.h"
#include "itkVector.h"
#include "itkLandmarkDisplacementFieldSource.h"
#include "itkImageFileWriter.h"

#include <fstream>


int main( int argc, char * argv[] )
{

  if( argc < 3 )
    {
    std::cerr << "Missing Parameters " << std::endl;
    std::cerr << "Usage: " << argv[0];
    std::cerr << " landmarksFile fixedImage outputDisplacementField"
              << std::endl;
    return EXIT_FAILURE;
    }

  constexpr unsigned int Dimension = 2;
  using VectorComponentType = float;

  using VectorType = itk::Vector< VectorComponentType, Dimension >;

  using DisplacementFieldType = itk::Image< VectorType,  Dimension >;


  using PixelType = unsigned char;
  using FixedImageType = itk::Image< PixelType, Dimension >;

  using FixedReaderType = itk::ImageFileReader< FixedImageType >;


  FixedReaderType::Pointer fixedReader = FixedReaderType::New();

  fixedReader->SetFileName( argv[2] );

  try
    {
    fixedReader->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown " << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }


  FixedImageType::ConstPointer fixedImage = fixedReader->GetOutput();

  using FilterType = itk::LandmarkDisplacementFieldSource< DisplacementFieldType >;

  FilterType::Pointer filter = FilterType::New();

  filter->SetOutputSpacing( fixedImage->GetSpacing() );
  filter->SetOutputOrigin(  fixedImage->GetOrigin() );
  filter->SetOutputRegion(  fixedImage->GetLargestPossibleRegion() );
  filter->SetOutputDirection( fixedImage->GetDirection() );

  //  Create source and target landmarks.
  //
  using LandmarkContainerType = FilterType::LandmarkContainer;
  using LandmarkPointType = FilterType::LandmarkPointType;

  LandmarkContainerType::Pointer sourceLandmarks
                                               = LandmarkContainerType::New();
  LandmarkContainerType::Pointer targetLandmarks
                                               = LandmarkContainerType::New();
  std::ifstream pointsFile;
  pointsFile.open( argv[1] );

  LandmarkPointType sourcePoint;
  pointsFile >> sourcePoint;
  LandmarkPointType targetPoint;
  pointsFile >> targetPoint;

  unsigned int pointId = 0;
  while( !pointsFile.fail() )
    {
    sourceLandmarks->InsertElement( pointId, sourcePoint );
    targetLandmarks->InsertElement( pointId, targetPoint );
    pointId++;

    pointsFile >> sourcePoint;
    pointsFile >> targetPoint;
    }
  pointsFile.close();
  filter->SetSourceLandmarks( sourceLandmarks );
  filter->SetTargetLandmarks( targetLandmarks );

  try
    {
    filter->UpdateLargestPossibleRegion();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown " << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }

  // Write an image for regression testing
  using WriterType = itk::ImageFileWriter<  DisplacementFieldType  >;

  WriterType::Pointer writer = WriterType::New();
  writer->SetInput (  filter->GetOutput() );
  writer->SetFileName( argv[3] );
  filter->Print( std::cout );
  try
    {
    writer->Update();
    }
  catch( itk::ExceptionObject & excp )
    {
    std::cerr << "Exception thrown by writer" << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }
  return EXIT_SUCCESS;
//  Software Guide : EndLatex
}
